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de.hu.wbi.histoner</FONT>
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Class HistoneModification</H2>
<PRE>
<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
  <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>de.hu.wbi.histoner.HistoneModification</B>
</PRE>
<DL>
<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>&gt;</DD>
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<DL>
<DT><PRE>public class <B>HistoneModification</B><DT>extends <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A><DT>implements <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>&gt;</DL>
</PRE>

<P>
Represents a histone - modification; a histone modification consists of 
 <ul>
 <li> Histone number (1, 2A, 2B, 3, 3.3, 4, 5)</li>
 <li> Amino acid (Lysine, Arginine, Serine, Threonine and Glutamate) </li>
 <li> Position of the amino acid modification </li>
 <li> The modification itself (methylation, acetylation, etc.) </li>
 </ul>
<P>

<P>
<DL>
<DT><B>Version:</B></DT>
  <DD>1.0</DD>
<DT><B>Author:</B></DT>
  <DD>philippe</DD>
</DL>
<HR>

<P>
<!-- ======== NESTED CLASS SUMMARY ======== -->

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<CODE>static&nbsp;class</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A></B></CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Represents an amino acid</TD>
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<!-- ======== CONSTRUCTOR SUMMARY ======== -->

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<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#HistoneModification(java.lang.String)">HistoneModification</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;modificationString)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Creates a histone modification  from a string following the Brno nomenclature</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#HistoneModification(java.lang.String, java.lang.String, de.hu.wbi.histoner.HistoneModification.Residue, int, int, int, java.lang.String)">HistoneModification</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;histone,
                    <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;modification,
                    <A HREF="../../../../de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A>&nbsp;residue,
                    int&nbsp;aaposition,
                    int&nbsp;from,
                    int&nbsp;to,
                    <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;entity)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Creates a histone modification</TD>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#compareTo(de.hu.wbi.histoner.HistoneModification)">compareTo</A></B>(<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>&nbsp;o)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getAaposition()">getAaposition</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getEntity()">getEntity</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getFrom()">getFrom</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getHistone()">getHistone</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getModification()">getModification</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getModificationRegex()">getModificationRegex</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Builds a regular expression string consisting of all different modification terms.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getPatternId()">getPatternId</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getResidue()">getResidue</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#getTo()">getTo</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#hashCode()">hashCode</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#overlaps(de.hu.wbi.histoner.HistoneModification)">overlaps</A></B>(<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>&nbsp;other)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if two histone modifications do overlap.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A>&gt;</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#residueMapping()">residueMapping</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Mapping from different amino acid descriptors to the FASTA - one letter format</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#setPatternId(java.lang.String)">setPatternId</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;patternId)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#toBrnoString()">toBrnoString</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html#toString()">toString</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
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&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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<P>

<!-- ========= CONSTRUCTOR DETAIL ======== -->

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<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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<A NAME="HistoneModification(java.lang.String, java.lang.String, de.hu.wbi.histoner.HistoneModification.Residue, int, int, int, java.lang.String)"><!-- --></A><H3>
HistoneModification</H3>
<PRE>
public <B>HistoneModification</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;histone,
                           <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;modification,
                           <A HREF="../../../../de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A>&nbsp;residue,
                           int&nbsp;aaposition,
                           int&nbsp;from,
                           int&nbsp;to,
                           <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;entity)</PRE>
<DL>
<DD>Creates a histone modification
<P>
<DL>
<DT><B>Parameters:</B><DD><CODE>histone</CODE> - Name  of histoe (e.g. 2A or 3)<DD><CODE>modification</CODE> - Type of modification<DD><CODE>residue</CODE> - Amino acid residue<DD><CODE>aaposition</CODE> - Location on amino-acid level<DD><CODE>from</CODE> - Start position in text<DD><CODE>to</CODE> - End position in text<DD><CODE>entity</CODE> - String found in text</DL>
</DL>
<HR>

<A NAME="HistoneModification(java.lang.String)"><!-- --></A><H3>
HistoneModification</H3>
<PRE>
public <B>HistoneModification</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;modificationString)</PRE>
<DL>
<DD>Creates a histone modification  from a string following the Brno nomenclature
<P>
<DL>
<DT><B>Parameters:</B><DD><CODE>modificationString</CODE> - Histone modification in Brno nomenclature</DL>
</DL>

<!-- ============ METHOD DETAIL ========== -->

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<A NAME="residueMapping()"><!-- --></A><H3>
residueMapping</H3>
<PRE>
public static <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A>&gt; <B>residueMapping</B>()</PRE>
<DL>
<DD>Mapping from different amino acid descriptors to the FASTA - one letter format
<P>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Map<String, Residue> maps strings to one-letter amino.acids</DL>
</DD>
</DL>
<HR>

<A NAME="getModificationRegex()"><!-- --></A><H3>
getModificationRegex</H3>
<PRE>
public static <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getModificationRegex</B>()</PRE>
<DL>
<DD>Builds a regular expression string consisting of all different modification terms. E.g. me-?1|me-?2|me-?3|...
<P>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Regular expression describing all possible modification terms</DL>
</DD>
</DL>
<HR>

<A NAME="overlaps(de.hu.wbi.histoner.HistoneModification)"><!-- --></A><H3>
overlaps</H3>
<PRE>
public boolean <B>overlaps</B>(<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>&nbsp;other)</PRE>
<DL>
<DD>Checks if two histone modifications do overlap. This might happen for two reasons:
 <ul>
 <li>The phrase describes more than one modification</li>
 <li>The phrase describes only one modification, but is hit by several regular expressions -> Remove such hits</li>
 </ul>
<P>
<DD><DL>
</DL>
</DD>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>other</CODE> - Other histone modification to compare with
<DT><B>Returns:</B><DD>boolean True if the two modifications are overlapping</DL>
</DD>
</DL>
<HR>

<A NAME="hashCode()"><!-- --></A><H3>
hashCode</H3>
<PRE>
public int <B>hashCode</B>()</PRE>
<DL>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<HR>

<A NAME="equals(java.lang.Object)"><!-- --></A><H3>
equals</H3>
<PRE>
public boolean <B>equals</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</PRE>
<DL>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<HR>

<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>
<DL>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<HR>

<A NAME="toBrnoString()"><!-- --></A><H3>
toBrnoString</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toBrnoString</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>String Returns a string in Brno nomenclature</DL>
</DD>
</DL>
<HR>

<A NAME="compareTo(de.hu.wbi.histoner.HistoneModification)"><!-- --></A><H3>
compareTo</H3>
<PRE>
public int <B>compareTo</B>(<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>&nbsp;o)</PRE>
<DL>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true#compareTo(T)" title="class or interface in java.lang">compareTo</A></CODE> in interface <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../../de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>&gt;</CODE></DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<HR>

<A NAME="getHistone()"><!-- --></A><H3>
getHistone</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getHistone</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the name of the histone</DL>
</DD>
</DL>
<HR>

<A NAME="getModification()"><!-- --></A><H3>
getModification</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getModification</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the modification</DL>
</DD>
</DL>
<HR>

<A NAME="getResidue()"><!-- --></A><H3>
getResidue</H3>
<PRE>
public <A HREF="../../../../de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A> <B>getResidue</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the amino acid one letter  (e.g. L, R, ..)</DL>
</DD>
</DL>
<HR>

<A NAME="getAaposition()"><!-- --></A><H3>
getAaposition</H3>
<PRE>
public int <B>getAaposition</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the amino acid location</DL>
</DD>
</DL>
<HR>

<A NAME="getFrom()"><!-- --></A><H3>
getFrom</H3>
<PRE>
public int <B>getFrom</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the start position of the modification</DL>
</DD>
</DL>
<HR>

<A NAME="getTo()"><!-- --></A><H3>
getTo</H3>
<PRE>
public int <B>getTo</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the stop position of the modification</DL>
</DD>
</DL>
<HR>

<A NAME="getEntity()"><!-- --></A><H3>
getEntity</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getEntity</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the matched string (e.g. 'di-methylation of histone H3 lysine 27')</DL>
</DD>
</DL>
<HR>

<A NAME="getPatternId()"><!-- --></A><H3>
getPatternId</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getPatternId</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>Returns the responsible patternId for this String</DL>
</DD>
</DL>
<HR>

<A NAME="setPatternId(java.lang.String)"><!-- --></A><H3>
setPatternId</H3>
<PRE>
public void <B>setPatternId</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;patternId)</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>patternId</CODE> - Sets the responsible patternId</DL>
</DD>
</DL>
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